MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : STM_v1_0 [2].
Target metabolite : ocdca_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (4 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: STM3646 STM2927 STM1749 STM2463 STM2285 STM3526 STM4570 STM4326 STM2952 STM0321 STM2947 STM3709 STM1135 STM1570 STM4036 STM4183 STM0370 STM1448 STM1326 STM4062 STM4484 STM2317 STM3179 STM1480 STM4126 STM4578 STM2338 STM2466 STM4467 STM3802 STM2196 STM3240 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.277441 (mmol/gDw/h)
  Minimum Production Rate : 0.008699 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 17.348164
  EX_glc__D_e : 5.000000
  EX_nh4_e : 3.057442
  EX_pi_e : 0.246042
  EX_k_e : 0.049274
  EX_so4_e : 0.033843
  EX_mg2_e : 0.002190
  EX_fe2_e : 0.002033
  EX_ca2_e : 0.001314
  EX_cl_e : 0.001314
  EX_cu2_e : 0.000876
  EX_mn2_e : 0.000876
  EX_mobd_e : 0.000876
  EX_zn2_e : 0.000876
  EX_cobalt2_e : 0.000876

Product: (mmol/gDw/h)
  EX_h2o_e : 25.344196
  EX_co2_e : 17.695608
  EX_h_e : 2.360742
  EX_acald_e : 0.707817
  Auxiliary production reaction : 0.008699
  DM_hmfurn_c : 0.000124

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

Last updated: 27-Sep-2023
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